Currently when placing waypoints, you can either place them spatially or attach them to an object.
The problem is, that when you have more than one waypoint attached to an object, things start becoming problematic, as you can't synchronize to specific waypoints on the object, delete them, etc. You have to ensure that you're completely done with the waypoint, before you put a new one on top, otherwise you'll have to delete all waypoints on top of it to get to it.
As a solution I'm proposing a new edit mode that works like the group or synchronize tool, in the way that you drag a line from a waypoint to an object, which would be identical to attaching the waypoint to an object, but allows you to organize it in the editor, and delete it, synchronize it, etc.
At the moment, it's like this:
I'm proposing something like this:
The green lines indicate that the waypoints are attached to the building, and the functionality is identical to that of the first screenshot (That is, their actual placement in the mission editor is disregarded, and their position becomes the same as if they were attached to the building), except you're now able to organize them, delete them freely, make cycle waypoints that can point to the right ones, as well as synchronize them, etc.:
This is of course an addition to the regular attachment, not a replacement.